MDM RNA-seq Analysis Report
Note
RNAseq data from Adam Fields’ Laboratory, University of California San Diego (UCSD).
Summary
Number of samples: 180Groups: HIV- moderate cannabis, HIV- daily cannabis, HIV- naive to cannabis, HIV+ naive to cannabis, HIV+ daily cannabis, HIV+ moderate cannabisTreatments: CBD, CBDpIL1B, IL1B, THC, THCpIL1B, VehicleHIV status: HIVn, HIVpCannabis use: moderate, daily, naive
Workflow Overview
We processed the RNA-seq data from monocyte-derived macrophages (MDMs) using the following pipeline:
DESeq2 Model
The differential expression model used:
design(dds) ~ treatment + hiv_status + cannabis
treatment: vehicle, IL1b, CBD, THC, CBD+IL1B, THC+IL1b
hiv_status: HIV- vs HIV+
cannabis: naive, moderate, daily
Results
Volcano Plots
volcano_list[["cannabis_daily_vs_naive"]]PCA Plots
using ntop=500 top features by variance
using ntop=500 top features by variance
using ntop=500 top features by variance
using ntop=500 top features by variance
Top Genes Tables
DT::datatable(top20_list[["cannabis_daily_vs_naive"]], options = list(pageLength = 5, scrollX = TRUE), rownames = FALSE)
Note
- Only genes with padj < 0.05 and |log2FC| > 1 are labeled in volcano plots.
- PCA plots can be faceted by
hiv_statusto observe group separation.
- Interactive tables allow scrolling and sorting top genes for each contrast.